Registry of Open Data on AWS

Usage examples for all datasets listed in the Registry of Open Data on AWS tagged with long read sequencing.

The Singapore Nanopore Expression Data Set

Tutorials

Accessing the SG-NEx dataset on AWS by Ying Chen
Basecalling and analysing SG-NEx samples in S/BLOW5 format by Hasindu Gamaarachchi
Differential RNA modification analysis tutorial with xPore by Yu Song Chuah
Performing transcript discovery and quantification with Bambu by Min Hao Ling
RNA modification analysis tutorial with m6Anet by Yu Song Chuah

Tools & Applications

Bambu: Transcript discovery and quantification using long read RNA-Seq data by Ying Chen, Andre Sim et al.
JAFFAL: Detection of fusion genes from long read RNA-Seq data by Nadia M Davidson et al.
m6Anet: Identification of m6A from a single direct RNA-Seq sample by Christopher Hendra et al.
nf-core/nanoseq: A nanopore DNA and RNA-Seq demultiplexing, QC, alignment and analysis pipeline by Chelsea Sawyer et al.
xPore: Identification of differential RNA modification from direct RNA-Seq data by Ploy Pratanwanich et al.

Publications

A systematic benchmark of Nanopore long read RNA sequencing for transcript level analysis in human cell lines. by Ying Chen et al.
Beyond sequencing: machine learning algorithms extract biology hidden in Nanopore signal data. by Yuk Kei Wan et al.
Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. by Christopher Hendra et al.
Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore. by Ploy N Pratanwanich et al.
JAFFAL: Detecting fusion genes with long read transcriptome sequencing. by Nadia M Davidson et al.

Garvan Institute Long Read Sequencing Benchmark Data

Tutorials

Directly processing on an s3fs mount by Hasindu Gamaarachchi
Fetching subsets with slow5curl and samtools by Bonson Wong

Tools & Applications

buttery-eel: The buttery eel - a slow5 guppy basecaller wrapper by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
Slow5curl: library and tool for accessing remote BLOW5 files. by Wong, B., et al.
Slow5lib: toolkit slow5lib is a software library for reading & writing SLOW5 files. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
Slow5tools: toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.

Publications

Accelerated nanopore basecalling with SLOW5 data format. by Samarakoon, H., Ferguson, J.M., Gamaarachchi H. et al.
Fast nanopore sequencing data analysis with SLOW5. by Gamaarachchi, H., Samarakoon, H., Jenner, S.P. et al.
Flexible and efficient handling of nanopore sequencing signal data with slow5tools. by Samarakoon, H., Ferguson, J.M., Jenner, S.P. et al.
Streamlining remote nanopore data access with slow5curl by Wong, B., Ferguson, J.M., Do, J.Y. et al.

PubSeq - Public Sequence Resource

Tutorials

Tools & Applications

Publications

Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 during Border Quarantine and Air Travel, New Zealand (Aotearoa) by Eichler, N. et al.

DNAStack COVID19 SRA Data

Tutorials

Viral lineage assignment by Heather Ward
AWS BatchAmazon EC2Amazon S3

Tools & Applications

Viral AI by DNAstack

Reference data for HiFi human WGS

Tutorials

PacBio WGS Variant Pipeline README by Pacific Biosciences of California, Inc

Tools & Applications

Consolidated analysis with the PacBio WGS Variant Pipeline by Pacific Biosciences of California, Inc

Platinum Pedigree

Publications

Google Brain Genomics Sequencing Dataset for Benchmarking and Development

Publications

An Extensive Sequence Dataset of Gold-Standard Samples for Benchmarking and Development by Baid G., Nattestad M., Kolesnikov A., Goel S., Yang H., Chang P., and Carroll A (2020)

If you want to add a dataset or usage example to this registry, please follow the instructions on the Registry of Open Data on AWS GitHub repository or tell us about your project.